made read.tree not require a groupfile, if one is not given all seqs are assumed...

[mothur.git] / treemap.cpp

diff --git a/treemap.cpp b/treemap.cpp
index 00ae0e664ff5fb7d289893b445be08b5fd20c89a..52a90031d380fedddd275bd5ebbb6a3f8600964c 100644 (file)
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -13,11 +13,11 @@
 
  TreeMap::TreeMap(string filename) {
        groupFileName = filename;
-       openInputFile(filename, fileHandle);
+       m->openInputFile(filename, fileHandle);
 }
 
 /************************************************************/
- TreeMap::~TreeMap(){};
+ TreeMap::~TreeMap(){}
 
 /************************************************************/
 void TreeMap::readMap() {
@@ -26,10 +26,10 @@ void TreeMap::readMap() {
                while(fileHandle){
                        fileHandle >> seqName;                  //read from first column
                        fileHandle >> seqGroup;                 //read from second column
-                       
+
                        namesOfSeqs.push_back(seqName);
                        setNamesOfGroups(seqGroup);
-                                               
+                                       
                        treemap[seqName].groupname = seqGroup;  //store data in map
                        
                        it2 = seqsPerGroup.find(seqGroup);
@@ -39,11 +39,45 @@ void TreeMap::readMap() {
                                seqsPerGroup[seqGroup]++;
                        }
 
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
                fileHandle.close();
 }
 /************************************************************/
+void TreeMap::addSeq(string seqName, string seqGroup) {
+       
+               namesOfSeqs.push_back(seqName);
+               setNamesOfGroups(seqGroup);
+                                       
+               treemap[seqName].groupname = seqGroup;  //store data in map
+                       
+               it2 = seqsPerGroup.find(seqGroup);
+               if (it2 == seqsPerGroup.end()) { //if it's a new group
+                       seqsPerGroup[seqGroup] = 1;
+               }else {//it's a group we already have
+                       seqsPerGroup[seqGroup]++;
+               }
+}
+/************************************************************/
+void TreeMap::removeSeq(string seqName) {
+       
+       //erase name from namesOfSeqs
+       for (int i = 0; i < namesOfSeqs.size(); i++) {
+               if (namesOfSeqs[i] == seqName)  {
+                       namesOfSeqs.erase(namesOfSeqs.begin()+i);
+                       break;
+               }
+       }
+       
+       //decrement sequences in this group
+       string group = treemap[seqName].groupname;
+       seqsPerGroup[group]--;
+       
+       //remove seq from treemap
+       it = treemap.find(seqName);
+       treemap.erase(it);
+}
+/************************************************************/
 
 int TreeMap::getNumGroups() {
                        
@@ -116,11 +150,7 @@ bool TreeMap::isValidGroup(string groupname) {
                return false;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the TreeMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "TreeMap", "isValidGroup");
                exit(1);
        }
 }
@@ -134,11 +164,7 @@ void TreeMap::print(ostream& output){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "TreeMap", "print");
                exit(1);
        }
 }
@@ -162,13 +188,36 @@ void TreeMap::makeSim(GroupMap* groupmap) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function make. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "TreeMap", "makeSim");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the TreeMap class function make. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/************************************************************/
+void TreeMap::makeSim(ListVector* list) {
+       try {
+               //set names of groups
+               namesOfGroups.clear();
+               for(int i = 0; i < list->size(); i++) {
+                       namesOfGroups.push_back(list->get(i));
+               }
+               
+               //set names of seqs to names of groups
+               namesOfSeqs = namesOfGroups;
+               
+               // make map where key and value are both the group name since that what the tree.shared command wants
+               for (int i = 0; i < namesOfGroups.size(); i++) {
+                       treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
+                       seqsPerGroup[namesOfGroups[i]] = 1;
+               }
+               
+               numGroups = namesOfGroups.size();
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TreeMap", "makeSim");
                exit(1);
        }
 }
+
 /************************************************************/